[BiO BB] SCOP ids from PDB id
MAG at Stowers-Institute.org
Thu Jun 22 10:19:15 EDT 2006
If you really have only a few PDB ids.. you could go to SCOP site and
put them in the "Keyword search for SCOP entries" .. it will take you to
the scop entry for the respective PDB files.
The RCSB (PDB) site also gives you an option making the tabulated
report.. you could choose the options of "SCOP domain" for all the PDB
files of your interest and then look at the report.
Also, not a very elegant option but something that I tried for a larger
number of PDBids is to download the SCOP parseable file and write a
small script to "grep" for each pdb-id in this file.. It will come up
with the scop_id for each file..
Hopefully somebody else on the list will have a better method for
generating this result.
I could try to help if you wnat to try any of the above three options.
All the best !
Stowers Institute for Medical Research
Kansas city, MO -64110
bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformatics.org
[mailto:bio_bulletin_board-bounces+mag=stowers-institute.org at bioinformat
ics.org] On Behalf Of Pankaj
Sent: Thursday, June 22, 2006 5:56 AM
To: bio; bioperl
Subject: [BiO BB] SCOP ids from PDB id
I have a few PDB ids.
I want to know whether these structures are related or not.
One way was to do it by calculating RMSD among all of them and seeing if
they r related or not. Other way was to get their SCOP id's and comapre
if they belong to same SCOP family. My question is given a PDB id, how
do I get its SCOP id? Thanking all in advance,
National Institute of Immunology
Open WebMail Project (http://openwebmail.org)
Bioinformatics.Org general forum -
BiO_Bulletin_Board at bioinformatics.org
More information about the BBB